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sgkit-dev / sgkit

Scalable genetics toolkit
https://sgkit-dev.github.io/sgkit
Apache License 2.0
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read_scikit_allel_vcfzarr returns string pad values instead of missing for INFO fields #1195

Open jeromekelleher opened 4 months ago

jeromekelleher commented 4 months ago

For example, in the test test_vcf_scikit_allel.py::test_all_fields, the variant_AA field is reported as ['' '' '' '' 'T' 'T' 'G' '' ''] instead of ['.' '.' '.' '.' 'T' 'T' 'G' '.' '.']

I'm not sure if this generalises to other fields, just reporting test breakage seen while fixing #1192